Japan says that China's new air defence identification zone are "not valid at all" and should be disregarded.
Singapore Airlines and Qantas have said that they will abide by the new rules.Both All Nippon Airlines (ANA) and Japan Airlines have been informing China's aviation authorities of flights through it since the weekend.
But the two airlines now say that they will stop doing so from Wednesday.
The zone includes disputed islands known as Senkaku in Japan and Diaoyu in China. Taiwan also claims the islands, which are controlled by Japan.
Part of the zone also overlaps with a submerged rock claimed by South Korea.
China says aircraft entering the zone must obey its rules, which include providing a flight plan, maintaining two-way radio communications and clearly identifying their nationality.
Aircraft who ignore the rules would be subject to "defensive emergency measures", China's Defence Ministry had said.